U.S. flag

An official website of the United States government
bit Xplor-NIH VMD-XPLOR
Pydoc: module psolPotTools
 
psolPotTools		 index


 
Tools to aid in setup/analysis of the Solvent Paramagnetic Relaxation
Enhancement potential term.
 
This module provides functions to simplify the creation, manipulation and
analysis of psolPot.PSolPot potential terms.

 
Functions
       
analyze(potList)
Perform analysis of PSolPot terms and return nicely formatted summary.
correlation(term)
create_PSolPot(name, file=None, restraints='', tauc=0.2, probeR=5.4, probeC=4.0, fixTauc=True, eSpinQuantumNumber=3.5, domainSelection='known and not pseudo')
Create an psolPot.PSolPot with given name, given the filename of an
PRE assignment table and/or a string of assignments.
 
  tauc               - correlation time
  probeR             - radius of probe molecule
  probeC             - probe concentration - units?
  fixTauc            - whether to fix the value of tauc, or to let it float
  eSpinQuantumNumber - electron sping quantum number
  domainSelection    - atoms to use in surface calculation
fitRho0(term, weighted=False)
For the given psolPot.PsolPot term, set rho0 such that term.rms()
is optimal. If weighted=True, the computed rho0 instead optimizes a
weighted rmsd:
 
  rmsd_w = sum_i w_i (Gamma_i - Gamma_i^obs)^2
 
where w_i = 1 / err_i^2. With weighted=True, restraints with err=0 are
excluded from this calculation.
qFactor(term)
tauc(term)